Plan for Fiordland BRUV FLD25

Setup

library(googlesheets4)
library(sf)
library(sfheaders)
library(tidyverse)
library(southernMaps)
library(mapview)
library(terra)
library(tidyterra)
library(rcartocolor)
library(ggnewscale)
library(ggspatial)
library(kableExtra)
library(ggrepel)
theme_set(theme_bw())

Load NZ coastline data

… and convert to sf object.

nztm <- detailed_nz_islands |> st_as_sf()

Marine reserves data

load(file = "data/mr_fiordland.Rdata")

Load strata

strata <- st_read("data/FLD25_Strata.kml")

Reading layer `Strata' from data source 
  `C:\git_projects\fiordland_bruv\data\FLD25_Strata.kml' using driver `KML'
Simple feature collection with 13 features and 2 fields
Geometry type: POLYGON
Dimension:     XYZ
Bounding box:  xmin: 166.3883 ymin: -45.8432 xmax: 167.0177 ymax: -45.47082
z_range:       zmin: 0 zmax: 0
Geodetic CRS:  WGS 84

plot(strata)

Load mark

mark <- png::readPNG("img/mark_blank.png") |> grid::rasterGrob(interpolate=TRUE)

BRUV data

Load from Google Sheet

… and convert to sf object.

fld24 <- read_sheet(
  "https://docs.google.com/spreadsheets/d/1IQfLTiWTQnTGynuF7fUu8htJxKZuIVJw4OK6y9qRfU8",
  sheet="FLD24") |> 
  mutate(Depth = coalesce(`Depth sensor`,`Depth sounder`)) |> 
  st_as_sf(coords = c('Longitude','Latitude'), crs=4326) |> 
  st_join(strata["Name"]) |> 
  filter(Quality %in% c("Good", "OK"))

Write full dataset to csv file (for copying stratum column into BRUVmetadata – actually nah)

read_sheet(
  "https://docs.google.com/spreadsheets/d/1IQfLTiWTQnTGynuF7fUu8htJxKZuIVJw4OK6y9qRfU8",
  sheet="FLD24") |> 
  mutate(Depth = coalesce(`Depth sensor`,`Depth sounder`)) |> 
  st_as_sf(coords = c('Longitude','Latitude'), crs=4326) |> 
  st_join(strata["Name"]) |> 
  write_csv(file = "data/fld24_strata.csv")

✔ Reading from "BRUVmetadata".

✔ Range ''FLD24''.

st_as_s2(): dropping Z and/or M coordinate

Export data for printing

dstrat <- c("DZ1","DZ2","DR2","DZ3","DZ4" )

decimal_to_dm <- function(decimal_degrees) {
  degrees <- floor(decimal_degrees)
  minutes <- (decimal_degrees - degrees) * 60
  return(paste0(degrees, "° ", formatC(minutes, format = "f", digits = 3), "'"))
}

fld24_toprint <- fld24 |>
  filter(Quality != "BAD") |> 
  as_data_frame() |> 
  transmute(
    SiteID,
    SetRep = substring(OpCode, 7, 13),
    Loc = Location,
    Stratum = Name |> 
      fct_relevel(dstrat),
    Depth,
    lat = st_coordinates(fld24)[,2] |> round(5),
    lon = st_coordinates(fld24)[,1] |> round(5),
    lat2 = st_coordinates(fld24)[,2] |> decimal_to_dm(),
    lon2 = st_coordinates(fld24)[,1] |> decimal_to_dm()
    
  ) |> 
  arrange(Stratum)

Warning: `as_data_frame()` was deprecated in tibble 2.0.0.
ℹ Please use `as_tibble()` (with slightly different semantics) to convert to a
  tibble, or `as.data.frame()` to convert to a data frame.

kable(fld24_toprint)

SiteID	SetRep	Loc	Stratum	Depth	lat	lon	lat2	lon2
LC01	S02_R01	Luncheon Cove	DZ1	35.9	-45.77672	166.4945	-46° 13.397’	166° 29.670’
LC02	S02_R02	Luncheon Cove	DZ1	23.0	-45.77042	166.4982	-46° 13.775’	166° 29.891’
LC03	S02_R03	Luncheon Cove	DZ1	34.0	-45.77522	166.5058	-46° 13.487’	166° 30.345’
LC08	S02_R05	Luncheon Cove	DZ1	40.0	-45.76553	166.5292	-46° 14.068’	166° 31.751’
LC06	S02_R06	Luncheon Cove	DZ1	42.0	-45.77145	166.5326	-46° 13.713’	166° 31.955’
AI08	S03_R02	Anchor Island	DZ1	21.0	-45.73870	166.5252	-46° 15.678’	166° 31.514’
AI09	S03_R03	Anchor Island	DZ1	38.0	-45.74827	166.5181	-46° 15.104’	166° 31.084’
AI10	S03_R04	Anchor Island	DZ1	28.0	-45.74457	166.5100	-46° 15.326’	166° 30.599’
AI11	S03_R05	Anchor Island	DZ1	71.0	-45.74618	166.5016	-46° 15.229’	166° 30.094’
AI12	S03_R06	Anchor Island	DZ1	71.0	-45.75023	166.5000	-46° 14.986’	166° 30.003’
AI01	S04_R01	Anchor Island	DZ1	41.8	-45.75005	166.5258	-46° 14.997’	166° 31.549’
AI02	S04_R02	Anchor Island	DZ1	79.0	-45.74478	166.5167	-46° 15.313’	166° 31.000’
AI03	S04_R03	Anchor Island	DZ1	20.0	-45.74017	166.5253	-46° 15.590’	166° 31.518’
LC04	S05_R04	Luncheon Cove	DZ1	86.0	-45.77767	166.5152	-46° 13.340’	166° 30.910’
LC05	S05_R05	Luncheon Cove	DZ1	45.0	-45.77575	166.5234	-46° 13.455’	166° 31.406’
LC07	S05_R06	Luncheon Cove	DZ1	30.0	-45.76930	166.5201	-46° 13.842’	166° 31.206’
OF01	S22_R01	Outer Five Fingers	DZ1	34.0	-45.71893	166.4898	-46° 16.864’	166° 29.391’
OF02	S22_R02	Outer Five Fingers	DZ1	44.0	-45.72385	166.4839	-46° 16.569’	166° 29.035’
OF03	S22_R03	Outer Five Fingers	DZ1	25.0	-45.72788	166.4762	-46° 16.327’	166° 28.573’
OF04	S22_R04	Outer Five Fingers	DZ1	34.0	-45.73192	166.4712	-46° 16.085’	166° 28.275’
OF05	S22_R05	Outer Five Fingers	DZ1	17.0	-45.73392	166.4650	-46° 15.965’	166° 27.902’
OF06	S22_R06	Outer Five Fingers	DZ1	31.0	-45.73877	166.4598	-46° 15.674’	166° 27.586’
EA02	S01_R02	East Anchor	DZ2	23.0	-45.76108	166.5369	-46° 14.335’	166° 32.212’
EA03	S01_R03	East Anchor	DZ2	79.0	-45.75900	166.5446	-46° 14.460’	166° 32.677’
EA08	S01_R04	East Anchor	DZ2	17.0	-45.77003	166.5534	-46° 13.798’	166° 33.207’
EA05	S01_R05	East Anchor	DZ2	65.0	-45.76277	166.5631	-46° 14.234’	166° 33.788’
EA06	S01_R06	East Anchor	DZ2	86.0	-45.76553	166.5525	-46° 14.068’	166° 33.151’
AI07	S03_R01	Anchor Island	DZ2	49.1	-45.73245	166.5272	-46° 16.053’	166° 31.631’
AI04	S04_R04	Anchor Island	DZ2	83.0	-45.73032	166.5401	-46° 16.181’	166° 32.407’
AI05	S04_R05	Anchor Island	DZ2	54.0	-45.74125	166.5464	-46° 15.525’	166° 32.786’
AI06	S04_R06	Anchor Island	DZ2	29.0	-45.74172	166.5556	-46° 15.497’	166° 33.333’
EA01	S05_R01	East Anchor	DZ2	57.0	-45.76440	166.5409	-46° 14.136’	166° 32.455’
EA04	S05_R02	East Anchor	DZ2	30.0	-45.75715	166.5584	-46° 14.571’	166° 33.505’
EA07	S05_R03	East Anchor	DZ2	38.0	-45.75388	166.5717	-46° 14.767’	166° 34.304’
RI01	S08_R01	Resolution Island	DZ2	19.2	-45.72102	166.5831	-46° 16.739’	166° 34.987’
RI02	S08_R02	Resolution Island	DZ2	34.0	-45.71980	166.5733	-46° 16.812’	166° 34.396’
PP02	S08_R05	Pigeon & Parrot Islands	DZ2	40.0	-45.71513	166.5280	-46° 17.092’	166° 31.681’
PP03	S08_R06	Pigeon & Parrot Islands	DZ2	32.0	-45.72005	166.5267	-46° 16.797’	166° 31.605’
LI02	S17_R02	Long Island	DZ2	30.0	-45.77093	166.6043	-46° 13.744’	166° 36.256’
LI03	S17_R03	Long Island	DZ2	23.0	-45.77240	166.6003	-46° 13.656’	166° 36.016’
LI04	S17_R04	Long Island	DZ2	25.0	-45.77600	166.6013	-46° 13.440’	166° 36.076’
PH01	S19_R01	Pickersgill Harbour	DZ2	31.5	-45.79447	166.5908	-46° 12.332’	166° 35.445’
PH02	S19_R02	Pickersgill Harbour	DZ2	33.0	-45.79415	166.5842	-46° 12.351’	166° 35.051’
PH03	S19_R03	Pickersgill Harbour	DZ2	42.0	-45.79445	166.5934	-46° 12.333’	166° 35.602’
PH04	S19_R04	Pickersgill Harbour	DZ2	32.0	-45.78363	166.5830	-46° 12.982’	166° 34.981’
PH05	S19_R05	Pickersgill Harbour	DZ2	81.0	-45.78190	166.6001	-46° 13.086’	166° 36.005’
ES01	S21_R01	Earshell Cove	DZ2	31.2	-45.72475	166.5894	-46° 16.515’	166° 35.366’
ES02	S21_R02	Earshell Cove	DZ2	48.0	-45.72678	166.5842	-46° 16.393’	166° 35.055’
ES03	S21_R03	Earshell Cove	DZ2	21.0	-45.73117	166.5777	-46° 16.130’	166° 34.661’
ES04	S21_R04	Earshell Cove	DZ2	46.0	-45.73853	166.5701	-46° 15.688’	166° 34.204’
ES05	S21_R05	Earshell Cove	DZ2	60.0	-45.74320	166.5735	-46° 15.408’	166° 34.412’
ES06	S21_R06	Earshell Cove	DZ2	52.7	-45.74770	166.5760	-46° 15.138’	166° 34.558’
FH01	S23_R01	Fixed Head	DZ2	25.0	-45.76270	166.5871	-46° 14.238’	166° 35.224’
FH02	S23_R02	Fixed Head	DZ2	45.0	-45.75477	166.6083	-46° 14.714’	166° 36.497’
FH03	S23_R03	Fixed Head	DZ2	18.0	-45.74933	166.6143	-46° 15.040’	166° 36.860’
FF01	S06_R01	Five Fingers	DR2	31.1	-45.70582	166.5711	-46° 17.651’	166° 34.263’
FF02	S06_R02	Five Fingers	DR2	52.0	-45.70425	166.5616	-46° 17.745’	166° 33.697’
FF03	S06_R03	Five Fingers	DR2	63.0	-45.70360	166.5512	-46° 17.784’	166° 33.070’
FF04	S06_R04	Five Fingers	DR2	86.0	-45.70063	166.5412	-46° 17.962’	166° 32.471’
FF05	S06_R05	Five Fingers	DR2	25.0	-45.69333	166.5438	-46° 18.400’	166° 32.628’
FF06	S06_R06	Five Fingers	DR2	18.0	-45.69175	166.5565	-46° 18.495’	166° 33.392’
FF07	S07_R01	Five Fingers	DR2	28.5	-45.68888	166.5305	-46° 18.667’	166° 31.831’
FF08	S07_R02	Five Fingers	DR2	28.0	-45.69353	166.5240	-46° 18.388’	166° 31.437’
FF09	S07_R03	Five Fingers	DR2	27.0	-45.69867	166.5181	-46° 18.080’	166° 31.087’
FF10	S07_R04	Five Fingers	DR2	26.0	-45.70330	166.5104	-46° 17.802’	166° 30.627’
FF11	S07_R05	Five Fingers	DR2	18.0	-45.70938	166.5012	-46° 17.437’	166° 30.072’
FF12	S07_R06	Five Fingers	DR2	41.0	-45.71433	166.4979	-46° 17.140’	166° 29.872’
RI03	S08_R03	Resolution Island	DR2	25.0	-45.71353	166.5591	-46° 17.188’	166° 33.545’
PP01	S08_R04	Pigeon & Parrot Islands	DR2	39.0	-45.70965	166.5481	-46° 17.421’	166° 32.887’
SI05	S09_R05	Shag Island	DZ3	35.0	-45.74290	166.7680	-46° 15.426’	166° 46.080’
SI06	S09_R06	Shag Island	DZ3	28.0	-45.74382	166.7570	-46° 15.371’	166° 45.418’
SI11	S15_R05	Shag Island	DZ3	64.0	-45.74245	166.7635	-46° 15.453’	166° 45.807’
SI12	S15_R06	Shag Island	DZ3	45.0	-45.74392	166.7555	-46° 15.365’	166° 45.331’
II01	S16_R01	Indian Island	DZ3	28.0	-45.76110	166.6465	-46° 14.334’	166° 38.788’
II02	S16_R02	Indian Island	DZ3	57.0	-45.76187	166.6405	-46° 14.288’	166° 38.433’
II03	S16_R03	Indian Island	DZ3	36.0	-45.76823	166.6378	-46° 13.906’	166° 38.271’
II04	S16_R04	Indian Island	DZ3	46.0	-45.76727	166.6315	-46° 13.964’	166° 37.890’
II05	S16_R05	Indian Island	DZ3	28.0	-45.77097	166.6236	-46° 13.742’	166° 37.417’
II06	S16_R06	Indian Island	DZ3	47.0	-45.76517	166.6241	-46° 14.090’	166° 37.448’
LI01	S17_R01	Long Island	DZ3	14.2	-45.76587	166.6148	-46° 14.048’	166° 36.891’
LI05	S17_R05	Long Island	DZ3	38.0	-45.77637	166.6087	-46° 13.418’	166° 36.523’
LI06	S17_R06	Long Island	DZ3	69.0	-45.77782	166.6129	-46° 13.331’	166° 36.771’
CL01	S18_R01	Curlew Island	DZ3	38.7	-45.78558	166.6075	-46° 12.865’	166° 36.451’
CL02	S18_R02	Curlew Island	DZ3	42.0	-45.78937	166.6088	-46° 12.638’	166° 36.526’
CL03	S18_R03	Curlew Island	DZ3	38.0	-45.79812	166.6120	-46° 12.113’	166° 36.718’
CL04	S18_R04	Curlew Island	DZ3	21.0	-45.80265	166.5988	-46° 11.841’	166° 35.930’
CL05	S18_R05	Curlew Island	DZ3	33.0	-45.80528	166.5881	-46° 11.683’	166° 35.288’
CL06	S18_R06	Curlew Island	DZ3	68.0	-45.79398	166.5990	-46° 12.361’	166° 35.938’
PH06	S19_R06	Pickersgill Harbour	DZ3	79.0	-45.79087	166.6021	-46° 12.548’	166° 36.124’
DC01	S20_R01	Duck Cove	DZ3	25.0	-45.74697	166.6567	-46° 15.182’	166° 39.400’
DC02	S23_R04	Duck Cove	DZ3	46.0	-45.74255	166.6531	-46° 15.447’	166° 39.188’
DC03	S23_R05	Duck Cove	DZ3	17.0	-45.74692	166.6521	-46° 15.185’	166° 39.123’
DC04	S23_R06	Duck Cove	DZ3	45.0	-45.74880	166.6580	-46° 15.072’	166° 39.482’
BW01	S24_R01	Bowen Channel	DZ3	32.8	-45.73972	166.6971	-46° 15.617’	166° 41.826’
BW02	S24_R02	Bowen Channel	DZ3	53.0	-45.73017	166.7091	-46° 16.190’	166° 42.544’
BW03	S24_R03	Bowen Channel	DZ3	36.0	-45.72955	166.7153	-46° 16.227’	166° 42.918’
BW04	S24_R04	Bowen Channel	DZ3	20.0	-45.72763	166.7263	-46° 16.342’	166° 43.576’
BW05	S24_R05	Bowen Channel	DZ3	51.0	-45.73610	166.7239	-46° 15.834’	166° 43.432’
BW06	S24_R06	Bowen Channel	DZ3	22.0	-45.74022	166.7223	-46° 15.587’	166° 43.338’
SI01	S09_R01	Shag Island	DZ4	49.6	-45.74372	166.7880	-46° 15.377’	166° 47.280’
SI02	S09_R02	Shag Island	DZ4	29.0	-45.73778	166.7870	-46° 15.733’	166° 47.218’
SI03	S09_R03	Shag Island	DZ4	24.0	-45.73197	166.7870	-46° 16.082’	166° 47.219’
SI04	S09_R04	Shag Island	DZ4	36.0	-45.73337	166.7697	-46° 15.998’	166° 46.182’
EC01	S10_R01	East Cooper Island	DZ4	36.4	-45.73463	166.9211	-46° 15.922’	166° 55.268’
EC03	S10_R03	East Cooper Island	DZ4	30.0	-45.73527	166.8988	-46° 15.884’	166° 53.930’
EC04	S10_R04	East Cooper Island	DZ4	28.0	-45.73700	166.8860	-46° 15.780’	166° 53.157’
EC05	S10_R05	East Cooper Island	DZ4	70.0	-45.72872	166.8818	-46° 16.277’	166° 52.906’
EC06	S10_R06	East Cooper Island	DZ4	58.0	-45.72575	166.8994	-46° 16.455’	166° 53.962’
SC01	S11_R01	Supper Cove	DZ4	25.4	-45.70307	166.9534	-46° 17.816’	166° 57.202’
SC02	S11_R02	Supper Cove	DZ4	55.0	-45.70700	166.9553	-46° 17.580’	166° 57.318’
SC03	S11_R03	Supper Cove	DZ4	64.0	-45.71162	166.9528	-46° 17.303’	166° 57.168’
SC04	S11_R04	Supper Cove	DZ4	65.0	-45.70937	166.9479	-46° 17.438’	166° 56.877’
SC05	S11_R05	Supper Cove	DZ4	54.0	-45.70732	166.9435	-46° 17.561’	166° 56.612’
SC06	S11_R06	Supper Cove	DZ4	23.0	-45.70253	166.9462	-46° 17.848’	166° 56.773’
SH01	S12_R01	Shark Cove	DZ4	71.4	-45.72023	166.9660	-46° 16.786’	166° 57.959’
SH02	S12_R02	Shark Cove	DZ4	51.0	-45.71955	166.9714	-46° 16.827’	166° 58.284’
SH03	S12_R03	Shark Cove	DZ4	28.0	-45.71705	166.9761	-46° 16.977’	166° 58.567’
SH04	S12_R04	Shark Cove	DZ4	33.0	-45.72855	166.9508	-46° 16.287’	166° 57.050’
SH05	S12_R05	Shark Cove	DZ4	51.0	-45.73150	166.9468	-46° 16.110’	166° 56.808’
SH06	S12_R06	Shark Cove	DZ4	32.0	-45.72108	166.9484	-46° 16.735’	166° 56.902’
FB01	S13_R01	Cooper Island	DZ4	27.0	-45.73793	166.8813	-46° 15.724’	166° 52.881’
FB02	S13_R02	Cooper Island	DZ4	45.0	-45.74085	166.8779	-46° 15.549’	166° 52.673’
FB03	S13_R03	Cooper Island	DZ4	52.0	-45.74118	166.8691	-46° 15.529’	166° 52.148’
FB04	S13_R04	Cooper Island	DZ4	27.0	-45.75247	166.8626	-46° 14.852’	166° 51.757’
FB05	S13_R05	Fanny Bay	DZ4	62.0	-45.76213	166.8347	-46° 14.272’	166° 50.083’
FB06	S13_R06	Fanny Bay	DZ4	71.0	-45.77178	166.8419	-46° 13.693’	166° 50.514’
NC01	S14_R01	North Cooper Island	DZ4	55.0	-45.71055	166.8425	-46° 17.367’	166° 50.547’
NC02	S14_R02	North Cooper Island	DZ4	32.0	-45.70575	166.8288	-46° 17.655’	166° 49.729’
NC03	S14_R03	North Cooper Island	DZ4	85.0	-45.71613	166.7994	-46° 17.032’	166° 47.963’
NC04	S14_R04	North Cooper Island	DZ4	18.0	-45.71837	166.7825	-46° 16.898’	166° 46.952’
NC05	S14_R05	North Cooper Island	DZ4	28.0	-45.72338	166.7607	-46° 16.597’	166° 45.640’
NC06	S14_R06	North Cooper Island	DZ4	18.0	-45.72658	166.7987	-46° 16.405’	166° 47.924’
SI07	S15_R01	Shag Island	DZ4	42.1	-45.72988	166.7899	-46° 16.207’	166° 47.394’
SI08	S15_R02	Shag Island	DZ4	36.0	-45.73352	166.7811	-46° 15.989’	166° 46.869’
SI09	S15_R03	Shag Island	DZ4	46.0	-45.73128	166.7773	-46° 16.123’	166° 46.637’
SI10	S15_R04	Shag Island	DZ4	15.0	-45.73295	166.7671	-46° 16.023’	166° 46.026’

# fld24_toprint |> write_csv(file = "data/fld24_toprint.csv")

First mapviews

mapview(fld24)

map_fiordland24 <- fld24 |> 
  mutate(Depth = -Depth) |> 
  mapview(zcol="Depth", layer.name = "BRUV drops (Depth)") +
  mapview(mr_fiordland |> 
            filter(Name %in% c(
              "Moana Uta (Wet Jacket Arm) Marine Reserve",
              "Taumoana (Five Finger Peninsula) Marine Reserve"
              )), 
          layer.name = "Marine Reserves", 
          col.region = "yellow")

map_fiordland24

saveRDS( map_fiordland24, "maps/map_fiordland24.rds")
mapshot(map_fiordland24, url = "maps/map_fiordland24.html")

nrow(fld24)

[1] 136

fld24 |> 
  group_by(Quality) |> 
  summarise(n = n())

Simple feature collection with 2 features and 2 fields
Geometry type: MULTIPOINT
Dimension:     XY
Bounding box:  xmin: 166.4598 ymin: -45.80528 xmax: 166.9761 ymax: -45.68888
Geodetic CRS:  WGS 84
# A tibble: 2 × 3
  Quality     n                                                         geometry
  <chr>   <int>                                                 <MULTIPOINT [°]>
1 Good      120 ((166.5305 -45.68888), (166.524 -45.69353), (166.5012 -45.70938…
2 OK         16 ((166.465 -45.73392), (166.4979 -45.71433), (166.6521 -45.74692…

fld24 |> 
  group_by(`Repeat site from 2021`) |> 
  summarise(n = n())

Simple feature collection with 2 features and 2 fields
Geometry type: MULTIPOINT
Dimension:     XY
Bounding box:  xmin: 166.4598 ymin: -45.80528 xmax: 166.9761 ymax: -45.68888
Geodetic CRS:  WGS 84
# A tibble: 2 × 3
  `Repeat site from 2021`     n                                         geometry
  <chr>                   <int>                                 <MULTIPOINT [°]>
1 No                        112 ((166.5305 -45.68888), (166.524 -45.69353), (16…
2 Yes                        24 ((166.5152 -45.77767), (166.5058 -45.77522), (1…

fld24  |>
  filter(Quality != "BAD") |> 
  summarise(
  min = min(Depth),
  max = max(Depth),
  mean = mean(Depth),
  median = median(Depth)
  )

Simple feature collection with 1 feature and 4 fields
Geometry type: MULTIPOINT
Dimension:     XY
Bounding box:  xmin: 166.4598 ymin: -45.80528 xmax: 166.9761 ymax: -45.68888
Geodetic CRS:  WGS 84
# A tibble: 1 × 5
    min   max  mean median                                              geometry
  <dbl> <dbl> <dbl>  <dbl>                                      <MULTIPOINT [°]>
1  14.2    86  40.8     36 ((166.5305 -45.68888), (166.524 -45.69353), (166.501…

Calculate areas

strata_clipped <- strata |> 
  st_transform(2193) |> 
  st_difference( nztm |> st_union() ) 

Warning: attribute variables are assumed to be spatially constant throughout
all geometries

plot(strata_clipped)

strata_areas <- strata_clipped |> 
  mutate( Area = ( strata |> st_area() / 1e6 ) |> units::drop_units()) |> 
  select(Name, Area) |> 
  st_drop_geometry()

st_as_s2(): dropping Z and/or M coordinate

strata_samples <- fld24 |> 
  filter(Quality != "Bad") |> 
  group_by(Name) |> 
  summarise(n = n()) |> 
  st_drop_geometry() |> 
  left_join(strata_areas) |> 
  mutate(
    Area = round(Area, 1),
    Sites_per_area = round(n / Area, 3)
    ) 

Joining with `by = join_by(Name)`

strata_samples

# A tibble: 5 × 4
  Name      n  Area Sites_per_area
  <chr> <int> <dbl>          <dbl>
1 DR2      14  23.2          0.603
2 DZ1      22  57.5          0.383
3 DZ2      33  54.8          0.602
4 DZ3      30  74.1          0.405
5 DZ4      37  76.1          0.486

kable(strata_samples)

Name	n	Area	Sites_per_area
DR2	14	23.2	0.603
DZ1	22	57.5	0.383
DZ2	33	54.8	0.602
DZ3	30	74.1	0.405
DZ4	37	76.1	0.486

fld24 |> filter(Quality != "Bad") |> ggplot() + aes(x=Depth) + geom_histogram() 

`stat_bin()` using `bins = 30`. Pick better value with `binwidth`.

fld24 |>
  filter(Quality != "Bad") |> 
  ggplot() + aes(x=Depth) + geom_histogram() + facet_wrap(vars(Name))

`stat_bin()` using `bins = 30`. Pick better value with `binwidth`.

Depths

fld24 |> 
  ggplot() +
  aes(x = `Depth sounder`, y = `Depth sensor`) +
  geom_point() +
  geom_abline(slope=1, intercept = 0)

Warning: Removed 24 rows containing missing values or values outside the scale range
(`geom_point()`).

Mappy map map

bathy_tamatea <- readRDS("data/bathy_tamatea.rds")

lim_tamatea_nzmg <- ext( c(2000000, 2042000, 5464000, 5488000) )

Points and strata 2024

ggmap_fld24_strata <- ggplot() +
  
  geom_spatraster(data = bathy_tamatea) +
  
  scale_fill_hypso_c(name = "Depth (m)", palette="colombia_bathy") +
  new_scale_fill() +
  
  geom_sf(
    data = strata |> 
      filter(Name %in% dstrat),
    aes(fill = Name),
    colour = 'black',
    alpha = .5
  ) +
  
  geom_sf(data = nztm, fill='grey40', colour=NA) +
  
  geom_sf(data = fld24, size = 2, color = "black") +
  
  geom_sf_text(
    data = strata |> 
      filter(Name %in% dstrat), 
    aes(label = Name), 
    colour = "white",
    nudge_y = c(-1500,0,0,0,0)) +  # Label strata
  
  scale_fill_brewer(name = "Stratum", palette = "Set2")  +

  # scale_fill_viridis_d(name = "Stratum", option = "C", alpha = 0.7) +
  
  scale_x_continuous(limits = lim_tamatea_nzmg[1:2], 
                     expand = c(0, 0)) +
  scale_y_continuous(limits = lim_tamatea_nzmg[3:4], 
                     expand = c(0, 0)) +
  
  annotation_scale(location = "br") +
  
  annotate("text", label = "Sea Through Science Ltd.") +
  
  xlab("") + ylab("")

<SpatRaster> resampled to 500760 cells.

ggmap_fld24_strata

ggmap_fld24_strata + 
  annotation_custom(mark, xmin = 2031500, xmax = 2042000, ymin = 5464000, ymax = 5470000)

ggsave("maps/map_fld24_strata.png", width = 10, height = 6, dpi = 300)

Strata with Breaksea too

get bbox

strata_nzmg <- strata |> 
  st_transform(strata, crs = 27200)

bbox_strata <- strata_nzmg |> 
  st_bbox()

bbox_strata

   xmin    ymin    xmax    ymax 
1995923 5464579 2042666 5507907 

ggmap_allstrata <- ggplot() +

  # geom_spatraster(data = bathy_tamatea, alpha = 0.1) +
  # 
  # scale_fill_hypso_c(name = "Depth (m)", palette="colombia_bathy") +
  # new_scale_fill() +
  
  geom_sf(
    data = strata_nzmg |> 
    st_transform(strata, crs = 27200),
    aes(fill = Name),
    colour = 'black',
    alpha = .5
  ) +
  
  geom_sf(data = nztm, fill='grey40', colour=NA) +
  
  geom_sf(data = fld24, size = 2, color = "black", alpha = .5) +
  
  geom_sf_text(
    data = strata,
    aes(label = Name),
    colour = "black",
    fontface = "bold",
    nudge_y = c(0,0,0,500,-1500,0,0,0,0,0,0,0,0)
    ) +  # Label strata
  
  # scale_fill_brewer(name = "Stratum", palette = "Set2")  +

  scale_x_continuous(limits = c(bbox_strata["xmin"], bbox_strata["xmax"]), 
                     expand = c(0, 0)) +
  scale_y_continuous(limits = c(bbox_strata["ymin"], bbox_strata["ymax"]), 
                     expand = c(0, 0)) +
  
  annotation_scale(location = "br") +
  
  annotate("text", label = "Sea Through Science Ltd.") +
  
  xlab("") + ylab("") +
  
  theme(legend.position = "none")

ggmap_allstrata

ggmap_allstrata + 
  annotation_custom(mark, xmin = 2031500, xmax = 2042000, ymin = 5464000, ymax = 5470000)

ggsave("maps/map_allstrata.png", width = 8, height = 8, dpi = 300)
ggsave("maps/map_allstrata.pdf", width = 8, height = 8)

Labelled map of 2024 sites

ggmap_fld24_labels <- 
  ggmap_fld24_strata +
  geom_label_repel(
    data = fld24, # |> 
      # mutate(
      #   X = st_coordinates(fld24)[,1],
      #   Y = st_coordinates(fld24)[,2]
      # ),
    aes(label = SiteID, geometry = geometry), 
    stat = "sf_coordinates",
    # size = 1,
    max.overlaps = 12,
    alpha = 0.6,
    box.padding = 0.05, 
    point.padding = 0.05,
    min.segment.length = 0)
 
ggmap_fld24_labels

ggmap_fld24_labels + 
  annotation_custom(mark, xmin = 2031500, xmax = 2042000, ymin = 5464000, ymax = 5470000)

ggsave("maps/map_fld24_labels.png", width = 18, height = 13, dpi = 300)
ggsave("maps/map_fld24_labels.pdf", width = 18, height = 13)

Points and reserves

ggmap_fld24 <- ggplot() +
  
  geom_spatraster(data = bathy_tamatea) +
  
  geom_sf(
    data = mr_fiordland, 
    fill = "yellow", col = NA, alpha = .3
    ) +
  
  geom_sf(data = nztm, fill='grey40', colour=NA) +
  
  geom_sf(
    data = fld24,
    size = 2
  ) +
  
  scale_fill_hypso_c(name = "Depth (m)", palette="colombia_bathy") +
  
  new_scale_fill() +
  
  scale_x_continuous(limits = lim_tamatea_nzmg[1:2], 
                     expand = c(0, 0)) +
  scale_y_continuous(limits = lim_tamatea_nzmg[3:4], 
                     expand = c(0, 0)) +
  
  annotation_scale(location = "br") +
  
  annotate("text", label = "Sea Through Science Ltd.")

<SpatRaster> resampled to 500760 cells.

ggmap_fld24

ggmap_fld24 + 
  annotation_custom(mark, xmin = 2031500, xmax = 2042000, ymin = 5464000, ymax = 5470000)

ggsave("maps/map_fld24.png", width = 10, height = 6, dpi = 300)